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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagtgtaatataaacttaagggttttaattgtgctgttttgactttgactgggctgtcttctaatcttctggatgttattgtggttgttgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG

Basic information

species Zea mays
transcript GRMZM2G108087_T01
intron # 3
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|89251975|gb|DY623761.1|DY623761
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|74235067|gb|DT642981.1|DT642981
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|211183486|gb|FL441241.1|FL441241
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|76286077|gb|DV025645.1|DV025645
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|78093274|gb|DV521648.1|DV521648
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAA
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAA
EST: gi|74234506|gb|DT642420.1|DT642420
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|74239521|gb|DT647435.1|DT647435
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|60336907|gb|DN203880.1|DN203880
EST:     CAGAGGGAGACGGCATATAAGCCAATTGTTCCACATAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|78117098|gb|DV535485.1|DV535485
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|211183485|gb|FL441240.1|FL441240
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|74234352|gb|DT642266.1|DT642266
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|78074309|gb|DV502743.1|DV502743
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|89756275|gb|DY686358.1|DY686358
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|71768040|gb|DR965977.1|DR965977
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 51

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgactgggctgtcttctaatcttctggatgttattgtggttgttgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG
               ttctaat  putative branch site (score: 124)
                             atgttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagtgtaatataaacttaagggttttaattgtgctgttttgactttgactgggctgtcttctaatcttctggatgttattgtggttgttgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggttg